config.txt

# The configuration file for srSim

# verbose - print detailed information (true/false)
verbose=true

# genomeLength - the length of the genome to simulate in nucleotides
genomeLength=10000000

# genome - the genome name to create reads
# if the filename exists, a genome will not be created
#genome=~/research_ccbb/trial3/yeast_reads_genome_bir.fasta
genome=genome.fasta

# avgRead - the average read length in nucleotides
# the average length for 454 pyrosequencing is 533
avgRead=50

# coverage - the coverage for the data
coverage=20

# machine - the machine used to sequence the data
# i.e. 454, illumina
machine=454

# qvdata - the qv data set to use
qvdata=454Data.txt

# mutation - can nucleotides be mutated? (true/false)
mutation=true

# qvScore - the default QV score for non-mutated simulations
qvScore=40

# printQV - should the program print a QV score?
printQV=false

# reverseCompliment - do you want ~50% of the reads to be reverse complimented?
reverseComplement=true

#threads - the number of threads to use (keep < 8)
threads=2